One of the main nucleic acid amplification techniques is the Polymerase Chain Reaction (PCR) (Saiki et al., Science, 230:1350-54 (1985)) taught in U.S. Pat. Nos. 4,683,202; 4,683,195; and 4,965,188, each incorporated herein by reference. Many commercial suppliers, including Fermentas, offer reagents for PCR.
PCR reaction mixture is basically assembled from the following components: nucleic acid target template, two or several target-specific oligonucleotides (primers), a thermophilic nucleic acid polymerase, deoxyribonucleoside triphosphates and a reaction buffer.
In each cycle of PCR amplification, a double-stranded target sequence is denatured, primers are annealed to each strand of the denatured target, and the primers are extended by the action of a DNA polymerase. DNA synthesis initiates at the accessible 3′-OH group of the target-specific oligonucleotides flanking the DNA sequence to be copied, thereby generating an identical copy of the target template nucleic acid sequence. The enzymatic reaction is repeated for a substantial number of thermal cycles consisting of the denaturation of the target nucleic acid, annealing of the primer oligonucleotides to complementary nucleic acid sequences and the subsequent extension of these primer-template complexes by the thermophilic nucleic acid polymerase.
Specificity of DNA amplification depends on the specificity of primer hybridization. Oligonucleotide primers for PCR are designed to be complementary to, or substantially complementary to, sequences occurring at the 3′ end of each strand of the target nucleic acid sequence. Hybridization of the primers with the target occurs usually at sufficiently high temperature to provide annealing conditions that ensure binding of the primers mainly to the complementary nucleic acid sequence of the target. However, PCR reaction mixtures are often assembled at room temperature, thus under less stringent oligonucleotide hybridization conditions. At room temperature, most thermophilic nucleic acid polymerases used for PCR possess a residual catalytic activity, which may cause degradation of primers and the formation of non specific byproducts, such as dimmers of primers or non-specific primer extension products. These unspecific PCR products can compete during subsequent PCR cycles with the specific PCR product for the primer molecules, DNA polymerase and nucleotides, thereby severely decreasing the efficiency of the amplification of the desired sequence (see, Chou et al., Nucleic Acids Research, 20(7): 1717-1723 (1992)).
A number of laborious, expensive and time-consuming approaches have been proposed to overcome difficulties related to the appearance of unspecific PCR byproducts. These so called “Hot Start” methods include physically separating reactants until annealing temperatures are reached, either manually (“manual hot-start PCR”), or by using wax (U.S. Pat. No. 5,411,876). Such procedures add a lot of extra time into the experimental process, and they also carry a higher risk of contamination due to the wax barrier itself or the requirement of opening the reaction vessel once some of the reactants have already been mixed and heated. Moreover, the formation of solid wax-barrier above the reaction mixture after finishing the PCR is less convenient for further sample processing.
Another method of reducing formation of unspecific extension products is a reversible inhibition of the DNA polymerase used in PCR. U.S. Pat. No. 5,338,671 discloses non-covalent modification of the nucleic acid polymerase by use of antibodies specific for said polymerase to inhibit the polymerase's activity. Pre-mixing of nucleic acid polymerase and polymerase-specific antibodies at room temperature results in the formation of antibody-polymerase complexes. Under these conditions, substantially no oligonucleotide extension by the DNA polymerase can be detected. At elevated temperatures, the antibodies become denatured and they dissociate from the complex, thereby releasing the active DNA polymerase. However, this method is expensive and carries the risk of contamination due to the possible presence of residual nucleic acids derived from the antibody preparation.
Several technologies for reversible covalent chemical inactivation of DNA polymerase, which becomes active only after incubation for a certain time period at elevated temperature, thus preventing production of PCR byproducts during the reaction set-up and the initial heating phase, are known in the prior art. It is generally considered that reversible chemical modification of DNA polymerase is the most convenient and preferred method for the “hot start” technique. Various modifying agents and modification conditions have been proposed that generate reversibly inactivated DNA polymerase with differing enzymatic characteristics that may be classified into two major groups of the modifying compounds:                1. protein acylation with dicarboxylic acid anhydrides (water based or organic solvent based reaction mixtures);        2. Protein modification with aldehydes resulting in the formation of Schiff bases.        
The chemically modified DNA polymerase disclosed in U.S. Pat. Nos. 5,677,152, 5,773,258, which are incorporated herein in their entirety by reference, is prepared in a single phase water-based system by treating the enzyme with the modifying reagent, dicarboxylic acid anhydride. However, this method requires quite strict control of the reaction conditions, such as pH, temperature and the reagent excess.
Alternative approach was disclosed in the U.S. Pat. No. 6,479,264, where dicarboxylic acid anhydride was used as a modifying reagent and the reaction was carried out in an anhydrous aprotic organic solvent.
Aldehydes, preferably the formaldehyde, are another group of modifying reagents that reversibly inactivate the thermophilic enzymes under essentially aqueous conditions, as taught in the U.S. Pat. No. 6,183,998. However, thermophilic DNA polymerase obtainable by such a modification is characterised by comparatively long reactivation times, up to 15 minutes at 94° C., what is sometimes undesirable for experimental purposes.